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SharingElectronMechanism.java

/* $Revision$ $Author$ $Date$
 * 
 * Copyright (C) 2008  Miguel Rojas <miguelrojasch@yahoo.es>
 * 
 * Contact: cdk-devel@lists.sourceforge.net
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. 
 */
package org.openscience.cdk.reaction.mechanism;

import java.util.ArrayList;
import java.util.List;

import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.ILonePair;
import org.openscience.cdk.interfaces.IMapping;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.reaction.IReactionMechanism;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.BondManipulator;

/**
 * <p>This mechanism displaces the charge (lonePair) because of
 * deficiency of charge. 
 * It returns the reaction mechanism which has been cloned the IMolecule.</p>
 * <p>This reaction could be represented as [A*]-B| => A=[B*]</p>
 * 
 * @author         miguelrojasch
 * @cdk.created    2008-02-10
 * @cdk.module     reaction
 *
 */
@TestClass(value="org.openscience.cdk.reaction.mechanism.SharingElectronMechanismTest")
00055 public class SharingElectronMechanism implements IReactionMechanism{

      /** 
     * Initiates the process for the given mechanism. The atoms to apply are mapped between
     * reactants and products. 
     *
     * @param moleculeSet The IMolecule to apply the mechanism
     * @param atomList    The list of atoms taking part in the mechanism. Only allowed two atoms                
     * @param bondList    The list of bonds taking part in the mechanism. Only allowed one bond
     * @return            The Reaction mechanism
     * 
       */
    @TestMethod(value="testInitiate_IMoleculeSet_ArrayList_ArrayList")
00068       public IReaction initiate(IMoleculeSet moleculeSet, ArrayList<IAtom> atomList,ArrayList<IBond> bondList) throws CDKException {
            CDKAtomTypeMatcher atMatcher = CDKAtomTypeMatcher.getInstance(moleculeSet.getBuilder());
            if (moleculeSet.getMoleculeCount() != 1) {
                  throw new CDKException("SharingElectronMechanism only expects one IMolecule");
            }
            if (atomList.size() != 2) {
                  throw new CDKException("SharingElectronMechanism expects two atoms in the ArrayList");
            }
            if (bondList.size() != 1) {
                  throw new CDKException("SharingElectronMechanism only expect one bond in the ArrayList");
            }
            IMolecule molecule = moleculeSet.getMolecule(0);
            IMolecule reactantCloned;
            try {
                  reactantCloned = (IMolecule) molecule.clone();
            } catch (CloneNotSupportedException e) {
                  throw new CDKException("Could not clone IMolecule!", e);
            }
            IAtom atom1 = atomList.get(0); // Atom containing the lone pair to share
            IAtom atom1C = reactantCloned.getAtom(molecule.getAtomNumber(atom1));
            IAtom atom2 = atomList.get(1); // Atom to neutralize the deficiency of charge
            IAtom atom2C = reactantCloned.getAtom(molecule.getAtomNumber(atom2));
            IBond bond1 = bondList.get(0);
            int posBond1 = molecule.getBondNumber(bond1);

            BondManipulator.increaseBondOrder(reactantCloned.getBond(posBond1));
            
            List<ILonePair> lonePair = reactantCloned.getConnectedLonePairsList(atom1C);
            reactantCloned.removeLonePair(lonePair.get(lonePair.size() -1));
            int charge = atom1C.getFormalCharge();
            atom1C.setFormalCharge(charge+1);
            
            charge = atom2C.getFormalCharge();
            atom2C.setFormalCharge(charge-1);
      
      atom1C.setHybridization(null);
            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);

            IAtomType type = atMatcher.findMatchingAtomType(reactantCloned, atom1C);
            if (type == null) return null;
            
            atom2C.setHybridization(null);
            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
            type = atMatcher.findMatchingAtomType(reactantCloned, atom2C);
            if (type == null) return null;
            
            IReaction reaction = DefaultChemObjectBuilder.getInstance().newReaction();
            reaction.addReactant(molecule);
            
            /* mapping */
            IMapping mapping = DefaultChemObjectBuilder.getInstance().newMapping(atom1, atom1C);
        reaction.addMapping(mapping);
        mapping = DefaultChemObjectBuilder.getInstance().newMapping(atom2, atom2C);
        reaction.addMapping(mapping);
        mapping = DefaultChemObjectBuilder.getInstance().newMapping(bond1, reactantCloned.getBond(posBond1));
      reaction.addMapping(mapping);
      reaction.addProduct(reactantCloned);
            
            return reaction;
      }

}

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